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T M. Murali - Publications

Affiliations: 
Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
Computer Science
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47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Law JN, Orbach SM, Weston BR, Steele PA, Rajagopalan P, Murali TM. Computational Construction of Toxicant Signaling Networks. Chemical Research in Toxicology. PMID 37471124 DOI: 10.1021/acs.chemrestox.2c00422  0.423
2022 Law JN, Akers K, Tasnina N, Santina CMD, Deutsch S, Kshirsagar M, Klein-Seetharaman J, Crovella M, Rajagopalan P, Kasif S, Murali TM. Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2. Gigascience. 10. PMID 34966926 DOI: 10.1093/gigascience/giab082  0.39
2021 Jalihal AP, Kraikivski P, Murali TM, Tyson JJ. Modeling and Analysis of the Macronutrient Signaling Network in Budding Yeast. Molecular Biology of the Cell. mbcE20020117. PMID 34495680 DOI: 10.1091/mbc.E20-02-0117  0.387
2020 Law JN, Kale SD, Murali TM. Accurate and efficient gene function prediction using a Multi-Bacterial network. Bioinformatics (Oxford, England). PMID 33063084 DOI: 10.1093/bioinformatics/btaa885  0.345
2020 Pratapa A, Jalihal AP, Law JN, Bharadwaj A, Murali TM. Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nature Methods. PMID 31907445 DOI: 10.1038/S41592-019-0690-6  0.501
2019 Franzese N, Groce A, Murali TM, Ritz A. Hypergraph-based connectivity measures for signaling pathway topologies. Plos Computational Biology. 15: e1007384. PMID 31652258 DOI: 10.1371/Journal.Pcbi.1007384  0.464
2019 Wagner MJ, Pratapa A, Murali TM. Reconstructing signaling pathways using regular language constrained paths. Bioinformatics (Oxford, England). 35: i624-i633. PMID 31510694 DOI: 10.1093/Bioinformatics/Btz360  0.428
2018 Wang L, Law J, Kale SD, Murali TM, Pandey G. Large-scale protein function prediction using heterogeneous ensembles. F1000research. 7. PMID 30450194 DOI: 10.12688/F1000Research.16415.1  0.339
2018 Huang LJ, Law JN, Murali TM. Automating the PathLinker app for Cytoscape. F1000research. 7: 727. PMID 30057757 DOI: 10.12688/F1000Research.14616.1  0.472
2018 Tegge AN, Rodrigues RR, Larkin AL, Vu L, Murali TM, Rajagopalan P. Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models. Scientific Reports. 8: 11306. PMID 30054499 DOI: 10.1038/S41598-018-29455-X  0.31
2017 Bharadwaj A, Singh DP, Ritz A, Tegge AN, Poirel CL, Kraikivski P, Adames N, Luther K, Kale SD, Peccoud J, Tyson JJ, Murali TM. GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinformatics (Oxford, England). 33: 3134-3136. PMID 28957495 DOI: 10.7490/F1000Research.1114636.1  0.774
2017 Gil DP, Law JN, Murali TM. The PathLinker app: Connect the dots in protein interaction networks. F1000research. 6: 58. PMID 28413614 DOI: 10.12688/F1000Research.9909.1  0.573
2016 Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM. Corrigendum: Pathway on demand: automated reconstruction of human signaling networks. Npj Systems Biology and Applications. 2: 16026. PMID 28731481 DOI: 10.1038/npjsba.2016.26  0.772
2016 Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM. Pathways on demand: automated reconstruction of human signaling networks. Npj Systems Biology and Applications. 2: 16002. PMID 28725467 DOI: 10.1038/npjsba.2016.2  0.778
2016 Sam SA, Teel J, Tegge AN, Bharadwaj A, Murali TM. XTalkDB: a database of signaling pathway crosstalk. Nucleic Acids Research. PMID 27899583 DOI: 10.1093/Nar/Gkw1037  0.391
2016 Tegge AN, Sharp N, Murali TM. Xtalk: a path-based approach for identifying crosstalk between signaling pathways. Bioinformatics (Oxford, England). 32: 242-51. PMID 26400040 DOI: 10.1093/Bioinformatics/Btv549  0.397
2016 Singh DP, Luther K, Murali TM. GraphCrowd: using crowds to design biological network visualizations F1000research. 5. DOI: 10.7490/F1000Research.1113484.1  0.398
2014 Murali T, Pacifico S, Finley RL. Integrating the interactome and the transcriptome of Drosophila. Bmc Bioinformatics. 15: 177. PMID 24913703 DOI: 10.1186/1471-2105-15-177  0.49
2014 Ritz A, Tegge AN, Kim H, Poirel CL, Murali TM. Signaling hypergraphs. Trends in Biotechnology. 32: 356-62. PMID 24857424 DOI: 10.1016/j.tibtech.2014.04.007  0.76
2014 Ritz A, Murali TM. Signaling hypergraphs for pathway reconstruction F1000research. 5. DOI: 10.7490/F1000Research.1096569.1  0.341
2014 Estep C, Yi J, Ritz A, Murali TM. GraphSpace: Sharing and collaborating through networks on the web Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 631-632. DOI: 10.1145/2649387.2660809  0.456
2014 Ritz A, Murali TM. Pathway analysis with signaling hypergraphs Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 249-258. DOI: 10.1109/Tcbb.2015.2459681  0.401
2013 Rahman A, Poirel CL, Badger DJ, Estep C, Murali TM. Reverse engineering molecular hypergraphs. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1113-24. PMID 24384702 DOI: 10.1109/Tcbb.2013.71  0.792
2013 Lasher CD, Rajagopalan P, Murali TM. Summarizing cellular responses as biological process networks. Bmc Systems Biology. 7: 68. PMID 23895181 DOI: 10.1186/1752-0509-7-68  0.507
2013 Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM. Top-down network analysis to drive bottom-up modeling of physiological processes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 409-18. PMID 23641868 DOI: 10.1089/Cmb.2012.0274  0.773
2013 Mairiang D, Zhang H, Sodja A, Murali T, Suriyaphol P, Malasit P, Limjindaporn T, Finley RL. Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. Plos One. 8: e53535. PMID 23326450 DOI: 10.1371/Journal.Pone.0053535  0.339
2013 Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM. Reconciling differential gene expression data with molecular interaction networks. Bioinformatics (Oxford, England). 29: 622-9. PMID 23314326 DOI: 10.1093/Bioinformatics/Btt007  0.79
2012 Murali TM. Computationally Driven Experimental Biology. Computer. 45: 22-23. PMID 24976642 DOI: 10.1109/Mc.2012.93  0.306
2012 Rivera CG, Tyler BM, Murali TM. Sensitive detection of pathway perturbations in cancers. Bmc Bioinformatics. 13: S9. PMID 22536907 DOI: 10.1186/1471-2105-13-S3-S9  0.762
2012 Yu J, Murali T, Finley RL. Assigning confidence scores to protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 812: 161-74. PMID 22218859 DOI: 10.1007/978-1-61779-455-1_9  0.375
2011 Poirel CL, Owens CC, Murali TM. Network-based functional enrichment. Bmc Bioinformatics. 12: S14. PMID 22479706 DOI: 10.1186/1471-2105-12-S13-S14  0.789
2011 Friedman AA, Tucker G, Singh R, Yan D, Vinayagam A, Hu Y, Binari R, Hong P, Sun X, Porto M, Pacifico S, Murali T, Finley RL, Asara JM, Berger B, et al. Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. Science Signaling. 4: rs10. PMID 22028469 DOI: 10.1126/Scisignal.2002029  0.453
2011 Dyer MD, Murali TM, Sobral BW. Supervised learning and prediction of physical interactions between human and HIV proteins. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 917-23. PMID 21382517 DOI: 10.1016/J.Meegid.2011.02.022  0.348
2011 Lasher CD, Rajagopalan P, Murali TM. Discovering networks of perturbed biological processes in hepatocyte cultures. Plos One. 6: e15247. PMID 21245926 DOI: 10.1371/Journal.Pone.0015247  0.469
2011 Murali T, Pacifico S, Yu J, Guest S, Roberts GG, Finley RL. DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Research. 39: D736-43. PMID 21036869 DOI: 10.1093/Nar/Gkq1092  0.477
2010 Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. Plos One. 5: e12089. PMID 20711500 DOI: 10.1371/Journal.Pone.0012089  0.729
2009 Driscoll T, Dyer MD, Murali TM, Sobral BW. PIG--the pathogen interaction gateway. Nucleic Acids Research. 37: D647-50. PMID 18984614 DOI: 10.1093/Nar/Gkn799  0.429
2009 Rivera CG, Murali TM. Identifying evolutionarily conserved protein interaction modules using graphhopper Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: 67-78. DOI: 10.1007/978-3-642-00727-9_9  0.701
2008 Murali TM, Rivera CG. Network legos: building blocks of cellular wiring diagrams. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 829-44. PMID 18707557 DOI: 10.1089/Cmb.2007.0139  0.793
2008 Dyer MD, Murali TM, Sobral BW. The landscape of human proteins interacting with viruses and other pathogens. Plos Pathogens. 4: e32. PMID 18282095 DOI: 10.1371/Journal.Ppat.0040032  0.409
2008 Jin Y, Murali TM, Ramakrishnan N. Compositional mining of multirelational biological datasets Acm Transactions On Knowledge Discovery From Data. 2. DOI: 10.1145/1342320.1342322  0.314
2006 Grothaus GA, Mufti A, Murali TM. Automatic layout and visualization of biclusters. Algorithms For Molecular Biology : Amb. 1: 15. PMID 16952321 DOI: 10.1186/1748-7188-1-15  0.33
2006 Massjouni N, Rivera CG, Murali TM. VIRGO: computational prediction of gene functions. Nucleic Acids Research. 34: W340-4. PMID 16845022 DOI: 10.1093/Nar/Gkl225  0.72
2006 Pati A, Vasquez-Robinet C, Heath LS, Grene R, Murali TM. XcisClique: analysis of regulatory bicliques. Bmc Bioinformatics. 7: 218. PMID 16630346 DOI: 10.1186/1471-2105-7-218  0.348
2004 Wu CJ, Fu Y, Murali TM, Kasif S. Gene expression module discovery using gibbs sampling. Genome Informatics. International Conference On Genome Informatics. 15: 239-48. PMID 15712126 DOI: 10.11234/Gi1990.15.239  0.305
2004 Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proceedings of the National Academy of Sciences of the United States of America. 101: 2888-93. PMID 14981259 DOI: 10.1073/Pnas.0307326101  0.394
2003 Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: Identification of diagnostic genes based on expression data Bioinformatics. 19: 1578-1579. PMID 12912841 DOI: 10.1093/Bioinformatics/Btg179  0.302
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